Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009638.1 Kokia drynarioides strain JFW-HI SEQ_124355, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 139407
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 8 characters in sequence are not A, C, G, or T
Found at i:4188 original size:56 final size:56
Alignment explanation
Indices: 4128--4252 Score: 153
Period size: 56 Copynumber: 2.2 Consensus size: 56
4118 GGTGAGCAAA
* * * *
4128 GGGATGACGAGTTGTGAACGCGGGAGAAGGCGAGCTATGGACATCAGGC-AGATAAG
1 GGGATGACGAGCTATGAACGCGGGAGAAGGCGAGCTATGGACATCAAGCGA-ACAAG
* * * * *
4184 GGGATGGCGAGCTATGGACGCGGGATAAGGCGAGTTGTGGACATCAAGCGAACAAG
1 GGGATGACGAGCTATGAACGCGGGAGAAGGCGAGCTATGGACATCAAGCGAACAAG
4240 GGGATGACGAGCT
1 GGGATGACGAGCT
4253 GTTGGGCTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
56 57 0.98
57 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.42, T:0.14
Consensus pattern (56 bp):
GGGATGACGAGCTATGAACGCGGGAGAAGGCGAGCTATGGACATCAAGCGAACAAG
Found at i:20289 original size:20 final size:20
Alignment explanation
Indices: 20266--20314 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
20256 ATATTTTTAA
20266 TATAA-TTTCTTTA-TATTTT
1 TATAATTTTC-TTACTATTTT
20285 CTATAATTTTCTTACTATTTT
1 -TATAATTTTCTTACTATTTT
20306 TATAATTTT
1 TATAATTTT
20315 TTCTAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (20 bp):
TATAATTTTCTTACTATTTT
Found at i:20324 original size:20 final size:19
Alignment explanation
Indices: 20266--20326 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 19
20256 ATATTTTTAA
*
20266 TATAATTTCTT-TATATTTT
1 TATAATTTTTTCTA-ATTTT
20285 CTATAATTTTCTTACT-ATTTT
1 -TATAATTTT-TT-CTAATTTT
*
20306 TATAATTTTTTCTAAATTT
1 TATAATTTTTTCTAATTTT
20325 TA
1 TA
20327 ATAAAATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
18 2 0.06
19 8 0.23
20 17 0.49
21 7 0.20
23 1 0.03
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (19 bp):
TATAATTTTTTCTAATTTT
Found at i:20346 original size:30 final size:30
Alignment explanation
Indices: 20310--20376 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
20300 TATTTTTATA
20310 ATTTTTTCTA-AATTTTAA-TAAAATTTAAAT
1 ATTTTTT-TATAATTTTAATTAAAATTT-AAT
*
20340 ATTTTTTTATAGTTTTAATTAAAATTTAAT
1 ATTTTTTTATAATTTTAATTAAAATTTAAT
*
20370 AATTTTT
1 ATTTTTT
20377 ATCTTTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 2 0.06
30 23 0.70
31 8 0.24
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (30 bp):
ATTTTTTTATAATTTTAATTAAAATTTAAT
Found at i:20346 original size:31 final size:30
Alignment explanation
Indices: 20307--20376 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
20297 TACTATTTTT
*
20307 ATAATTTTTTCTAAATTTTAA-TAAAATTTAA
1 ATAATTTTTTAT-AATTTTAATTAAAATTT-A
* *
20338 ATATTTTTTTATAGTTTTAATTAAAATTTA
1 ATAATTTTTTATAATTTTAATTAAAATTTA
20368 ATAATTTTT
1 ATAATTTTT
20377 ATCTTTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 16 0.47
31 18 0.53
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (30 bp):
ATAATTTTTTATAATTTTAATTAAAATTTA
Found at i:21359 original size:22 final size:21
Alignment explanation
Indices: 21305--21359 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
21295 TTTAGATCCT
21305 TTATAATTTATAAAATAAAAAA
1 TTATAATTTA-AAAATAAAAAA
* * * *
21327 TTTTAAATTAATAATGATAAAA
1 TTATAATTTAAAAAT-AAAAAA
21349 TTATAATTTAA
1 TTATAATTTAA
21360 CTTTCAAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
TTATAATTTAAAAATAAAAAA
Found at i:21381 original size:31 final size:31
Alignment explanation
Indices: 21345--21414 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 31
21335 TAATAATGAT
21345 AAAATTATAATTT-AACTTTCAAAAAATTATA
1 AAAATTATAATTTGAACTTT-AAAAAATTATA
* *
21376 AAAATT-TAATTTGATCTTTTAAAAATTATA
1 AAAATTATAATTTGAACTTTAAAAAATTATA
21406 AAAA-TATAA
1 AAAATTATAA
21415 ATTATTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 1 0.03
30 23 0.66
31 11 0.31
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (31 bp):
AAAATTATAATTTGAACTTTAAAAAATTATA
Found at i:21418 original size:15 final size:16
Alignment explanation
Indices: 21398--21431 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
21388 GATCTTTTAA
21398 AAATTATAAAAAT-AT
1 AAATTATAAAAATGAT
*
21413 AAATTATTAAAATGAT
1 AAATTATAAAAATGAT
21429 AAA
1 AAA
21432 ATTGTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATGAT
Found at i:21514 original size:25 final size:25
Alignment explanation
Indices: 21476--21524 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
21466 TGACCAATGT
21476 TACCTCATACTAATAATTTTCATAG
1 TACCTCATACTAATAATTTTCATAG
*
21501 TACCTCATATTAATAATTTTCATA
1 TACCTCATACTAATAATTTTCATA
21525 TGATTAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.18, G:0.02, T:0.43
Consensus pattern (25 bp):
TACCTCATACTAATAATTTTCATAG
Found at i:22916 original size:23 final size:22
Alignment explanation
Indices: 22884--22927 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
22874 AGTACCTATA
22884 CTTTAATTTTATCAATTTTAAT
1 CTTTAATTTTATCAATTTTAAT
* *
22906 CTTTATATTTTTTGAATTTTAA
1 CTTTA-ATTTTATCAATTTTAA
22928 AATTTTAGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (22 bp):
CTTTAATTTTATCAATTTTAAT
Found at i:33763 original size:25 final size:25
Alignment explanation
Indices: 33716--33763 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
33706 ATTGGGTTTG
* * *
33716 GTTTAATTTTTGATTTTTTATATTA
1 GTTTAATTTTTGATATATAATATTA
*
33741 GTTTAATTTTTTATATATAATAT
1 GTTTAATTTTTGATATATAATAT
33764 ATTAAAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (25 bp):
GTTTAATTTTTGATATATAATATTA
Found at i:40791 original size:13 final size:15
Alignment explanation
Indices: 40773--40804 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
40763 AGGAACGAAA
40773 AAATCC-CAAAA-AT
1 AAATCCTCAAAAGAT
40786 AAATCCTCAAAAGAT
1 AAATCCTCAAAAGAT
40801 AAAT
1 AAAT
40805 TAATTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 5 0.29
15 6 0.35
ACGTcount: A:0.59, C:0.19, G:0.03, T:0.19
Consensus pattern (15 bp):
AAATCCTCAAAAGAT
Found at i:56280 original size:26 final size:25
Alignment explanation
Indices: 56207--56281 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 25
56197 ATTGTTTATA
* *
56207 TTTTATATTTTTAATAATTTAATGAT
1 TTTTATATTTTTAAAAATTT-TTGAT
56233 TTTTAT-TTTTTAAAATATTTTTTGAAT
1 TTTTATATTTTTAAAA-A-TTTTTG-AT
*
56260 TTTTGTATTTTTAAAAATTTTT
1 TTTTATATTTTTAAAAATTTTT
56282 AAAATTAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
25 8 0.19
26 14 0.33
27 11 0.26
28 9 0.21
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (25 bp):
TTTTATATTTTTAAAAATTTTTGAT
Found at i:56287 original size:27 final size:27
Alignment explanation
Indices: 56231--56287 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
56221 TAATTTAATG
**
56231 ATTTTTATTTTTTAAAATATTTTTTGA
1 ATTTTTATTTTTTAAAATATTTTTAAA
*
56258 ATTTTTGTATTTTTAAAA-ATTTTTAAA
1 ATTTTTAT-TTTTTAAAATATTTTTAAA
56285 ATT
1 ATT
56288 AATTAAATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 17 0.65
28 9 0.35
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (27 bp):
ATTTTTATTTTTTAAAATATTTTTAAA
Found at i:57754 original size:21 final size:19
Alignment explanation
Indices: 57717--57755 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
57707 TCTAAATCTC
*
57717 TGTTTAACTATGTTTTCTT
1 TGTTTAACTATATTTTCTT
57736 TGTTGTAACTTATATTTTCT
1 TGTT-TAAC-TATATTTTCT
57756 CGATAGCCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 4 0.24
21 9 0.53
ACGTcount: A:0.18, C:0.10, G:0.10, T:0.62
Consensus pattern (19 bp):
TGTTTAACTATATTTTCTT
Found at i:60353 original size:19 final size:18
Alignment explanation
Indices: 60301--60354 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 18
60291 GTTGCACTGC
60301 ATGGACTTGACCAAGGCAA
1 ATGGACTTGACC-AGGCAA
*
60320 ATGGGACTTGTCCAGGCAAAA
1 AT-GGACTTGACCAGGC--AA
60341 ATGGACTT-ACCAGG
1 ATGGACTTGACCAGG
60355 TAGTAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 11 0.37
20 15 0.50
21 4 0.13
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.19
Consensus pattern (18 bp):
ATGGACTTGACCAGGCAA
Found at i:65999 original size:6 final size:6
Alignment explanation
Indices: 65988--66056 Score: 84
Period size: 6 Copynumber: 11.5 Consensus size: 6
65978 TGATCAAAAT
* * *
65988 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGAAAG TGAAAG
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG
* * *
66036 TGAAAT TGGAAC TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGA
66057 TATGAATTGA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.46, C:0.01, G:0.30, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:66019 original size:30 final size:30
Alignment explanation
Indices: 65985--66056 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
65975 TTGTGATCAA
65985 AATTGAAAGTGAAAGTGAAAGTGAAATTGG
1 AATTGAAAGTGAAAGTGAAAGTGAAATTGG
66015 AATTGAAAGTGAAAGTGAAAGTGAAATTGG
1 AATTGAAAGTGAAAGTGAAAGTGAAATTGG
*
66045 AACTGAAAGTGA
1 AATTGAAAGTGA
66057 TATGAATTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.47, C:0.01, G:0.29, T:0.22
Consensus pattern (30 bp):
AATTGAAAGTGAAAGTGAAAGTGAAATTGG
Found at i:66021 original size:18 final size:16
Alignment explanation
Indices: 65985--66068 Score: 58
Period size: 12 Copynumber: 5.5 Consensus size: 16
65975 TTGTGATCAA
65985 AATTGAAAGTGAAA-G
1 AATTGAAAGTGAAATG
66000 ---TGAAAGTGAAATTGG
1 AATTGAAAGTGAAA-T-G
66015 AATTGAAAGTGAAA-G
1 AATTGAAAGTGAAATG
66030 ---TGAAAGTGAAATTGG
1 AATTGAAAGTGAAA-T-G
* *
66045 AACTGAAAGTGATATG
1 AATTGAAAGTGAAATG
66061 AATTGAAA
1 AATTGAAA
66069 ATTGAAAATC
Statistics
Matches: 55, Mismatches: 2, Indels: 23
0.69 0.03 0.29
Matches are distributed among these distances:
12 22 0.40
15 3 0.05
16 8 0.15
17 1 0.02
18 21 0.38
ACGTcount: A:0.48, C:0.01, G:0.27, T:0.24
Consensus pattern (16 bp):
AATTGAAAGTGAAATG
Found at i:66021 original size:24 final size:24
Alignment explanation
Indices: 65984--66068 Score: 102
Period size: 24 Copynumber: 3.6 Consensus size: 24
65974 TTTGTGATCA
*
65984 AAATTGAAAGTGAAAGTGAAAGTG
1 AAATTGAAATTGAAAGTGAAAGTG
*
66008 AAATTGGAATTGAAAGTGAAAGTG
1 AAATTGAAATTGAAAGTGAAAGTG
* * *
66032 AAAGTGAAATTGGAACTGAAAGTG
1 AAATTGAAATTGAAAGTGAAAGTG
*
66056 ATA-TG-AATTGAAA
1 AAATTGAAATTGAAA
66069 ATTGAAAATC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
22 7 0.13
23 2 0.04
24 44 0.83
ACGTcount: A:0.48, C:0.01, G:0.27, T:0.24
Consensus pattern (24 bp):
AAATTGAAATTGAAAGTGAAAGTG
Found at i:68338 original size:19 final size:19
Alignment explanation
Indices: 68307--68343 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
68297 TCTATTTATT
68307 ATATGTTATTTTTAAATAC
1 ATATGTTATTTTTAAATAC
68326 ATAT-TTATGTTTTAAATA
1 ATATGTTAT-TTTTAAATA
68344 TACGATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (19 bp):
ATATGTTATTTTTAAATAC
Found at i:71727 original size:15 final size:15
Alignment explanation
Indices: 71687--71730 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
71677 TTAAATTAAA
*
71687 TTATAATTTTATTAT
1 TTATAATTTTATAAT
*
71702 TTAT-TTATTTATAAT
1 TTATAAT-TTTATAAT
71717 TTATAATTTTATAA
1 TTATAATTTTATAA
71731 AATTTAAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 1 0.04
15 22 0.92
16 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATAATTTTATAAT
Found at i:72102 original size:24 final size:23
Alignment explanation
Indices: 72041--72102 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
72031 TTTATTTAAC
*
72041 TTAATCGAATATGTTCACGAACA
1 TTAATCGAACATGTTCACGAACA
* *
72064 TTAAACGAACATGTTCATGAACA
1 TTAATCGAACATGTTCACGAACA
*
72087 TATAATTGAACATGTT
1 T-TAATCGAACATGTT
72103 TAGGAACAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
23 21 0.64
24 12 0.36
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAACA
Found at i:73004 original size:25 final size:27
Alignment explanation
Indices: 72959--73021 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 27
72949 AAAAAATTCA
* **
72959 AAAAAAAATA-ATACATGAATATTTTT
1 AAAAAATATATATACATGAATAAATTT
72985 AAAAAATATATATA-AT-AATAAATTT
1 AAAAAATATATATACATGAATAAATTT
*
73010 AAAAATTATATA
1 AAAAAATATATA
73022 AAAATAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 18 0.56
26 11 0.34
27 3 0.09
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (27 bp):
AAAAAATATATATACATGAATAAATTT
Found at i:86971 original size:139 final size:139
Alignment explanation
Indices: 86797--87075 Score: 495
Period size: 139 Copynumber: 2.0 Consensus size: 139
86787 TAAAAATTAA
* *
86797 AATTTATATTTATTAAACAATTTAATTATATTCCGTATATACTTTTAAGTAATATATGGTTGAGG
1 AATTTATATTTATTAAACAATTTAATTATATTCCGTAAATAATTTTAAGTAATATATGGTTGAGG
* *
86862 GGGCCAGCTCTCCTATTGAAAGAAGTCTTTGAAGTGTCATCCTCTAAGCAATTGATCGGATCCTC
66 GGGCCAGCTCTCCTATTGAAAAAAGTCTTTGAAGTGTCATCCTCTAAGCAATTGATCGAATCCTC
86927 GAATAGTGG
131 GAATAGTGG
86936 AATTTATATTTATTAAACAATTTAATTATATTCCGTAAATAATTTTAAGTAATATATGGTTGAGG
1 AATTTATATTTATTAAACAATTTAATTATATTCCGTAAATAATTTTAAGTAATATATGGTTGAGG
* **
87001 GGGTCAGCTCTTTTATTGAAAAAAGTCTTTGAAGTGTCATCCTCTAAGCAATTGATCGAATCCTC
66 GGGCCAGCTCTCCTATTGAAAAAAGTCTTTGAAGTGTCATCCTCTAAGCAATTGATCGAATCCTC
87066 GAATAGTGG
131 GAATAGTGG
87075 A
1 A
87076 GGTATTGTCC
Statistics
Matches: 133, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
139 133 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (139 bp):
AATTTATATTTATTAAACAATTTAATTATATTCCGTAAATAATTTTAAGTAATATATGGTTGAGG
GGGCCAGCTCTCCTATTGAAAAAAGTCTTTGAAGTGTCATCCTCTAAGCAATTGATCGAATCCTC
GAATAGTGG
Found at i:93662 original size:18 final size:17
Alignment explanation
Indices: 93635--93679 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
93625 CCGGTAAAAG
93635 TTTT-ATTAATTTAAATT
1 TTTTAATTAA-TTAAATT
*
93652 TTTTAATTAATTAATTT
1 TTTTAATTAATTAAATT
93669 TATTTAATTAA
1 T-TTTAATTAA
93680 AAATCTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAATTAATTAAATT
Found at i:94616 original size:55 final size:55
Alignment explanation
Indices: 94532--94637 Score: 160
Period size: 55 Copynumber: 1.9 Consensus size: 55
94522 TATCAAAAAG
* * *
94532 TTAGTTGGAATATAATTGACATGTCATAGGATACATGAGCTCATATAGTGTAATT
1 TTAGTCGGAATATAATTGACATATCATAGGATACATGAGCGCATATAGTGTAATT
*
94587 TTAGTCGGAGTATAATT-AGCATATCATAGGATACATGAGCGCATATAGTGT
1 TTAGTCGGAATATAATTGA-CATATCATAGGATACATGAGCGCATATAGTGT
94638 TATGGGGTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 1 0.02
55 45 0.98
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (55 bp):
TTAGTCGGAATATAATTGACATATCATAGGATACATGAGCGCATATAGTGTAATT
Found at i:106793 original size:71 final size:72
Alignment explanation
Indices: 106675--106816 Score: 164
Period size: 71 Copynumber: 2.0 Consensus size: 72
106665 TGGAATCGAC
* * * *
106675 TTTTTTACAAAAAATAATTTTTGATAGAAAAAGCTTTCAAGATTAATTACTAAGAGGCCT-CTCT
1 TTTTTTACAAAAAATAATTTTTGACAGAAAAAACTTTCAAGACTAATTACTAAGAGACCTCCT-T
106739 ATTTTTGA
65 ATTTTTGA
* ** **
106747 TTTTTTAC-AAAAATACTTTTTGACAGAAAAAACATTT-TGGACTAATTGGTAAGAGACCTCCTT
1 TTTTTTACAAAAAATAATTTTTGACAGAAAAAAC-TTTCAAGACTAATTACTAAGAGACCTCCTT
106810 ATTTTTG
65 ATTTTTG
106817 GTGTTAAAAG
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
71 46 0.78
72 13 0.22
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (72 bp):
TTTTTTACAAAAAATAATTTTTGACAGAAAAAACTTTCAAGACTAATTACTAAGAGACCTCCTTA
TTTTTGA
Found at i:107077 original size:29 final size:27
Alignment explanation
Indices: 107040--107095 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
107030 CAAATATCTA
107040 TTTTTGTAAGTAACCTATTTTTTATATT
1 TTTTTGTAAGTAA-CTATTTTTTATATT
* *
107068 TTTTTCGTAATTAATTATTTTTTATATT
1 TTTTT-GTAAGTAACTATTTTTTATATT
107096 ACTTGAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.64
Consensus pattern (27 bp):
TTTTTGTAAGTAACTATTTTTTATATT
Found at i:113406 original size:24 final size:24
Alignment explanation
Indices: 113374--113421 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
113364 ATTGCACTCC
113374 CAAAAAGAAAACACAGGTTTGAAG
1 CAAAAAGAAAACACAGGTTTGAAG
113398 CAAAAAGAAAACACAGGTTTGAAG
1 CAAAAAGAAAACACAGGTTTGAAG
113422 GAGATAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.12, G:0.21, T:0.12
Consensus pattern (24 bp):
CAAAAAGAAAACACAGGTTTGAAG
Found at i:113877 original size:2 final size:2
Alignment explanation
Indices: 113870--113895 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
113860 ATGTAATTCA
113870 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
113896 GTAGCAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:134040 original size:24 final size:24
Alignment explanation
Indices: 134013--134062 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
134003 TTTTGTATGT
* *
134013 AGAAACAGTAGAAACAAAAGAGAG
1 AGAAAAAGTAAAAACAAAAGAGAG
**
134037 AGAAAAAGTAAAAATTAAAGAGAG
1 AGAAAAAGTAAAAACAAAAGAGAG
134061 AG
1 AG
134063 CTTCACCAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.64, C:0.04, G:0.24, T:0.08
Consensus pattern (24 bp):
AGAAAAAGTAAAAACAAAAGAGAG
Done.